Selected Target Proteins Research Articles

Identification of marker genes in Alzheimer's disease using a machine-learning model.

Alzheimer's Disease (AD) is one of the most common causes of dementia, mostly affecting the elderly population. Currently, there is no proper diagnostic tool or method available for the detection of AD. The present study used two distinct data sets of AD genes, which could be potential biomarkers in the diagnosis. The differentially expressed genes (DEGs) curated from both datasets were used for machine learning classification, tissue expression annotation and co-expression analysis. Further, CNPY3, GPR84, HIST1H2AB, HIST1H2AE, IFNAR1, LMO3, MYO18A, N4BP2L1, PML, SLC4A4, ST8SIA4, TLE1 and N4BP2L1 were identified as highly significant DEGs and exhibited co-expression with other query genes. Moreover, a tissue expression study found that these genes are also expressed in the brain tissue. In addition to the earlier studies for marker gene identification, we have considered a different set of machine learning classifiers to improve the accuracy rate from the analysis. Amongst all the six classification algorithms, J48 emerged as the best classifier, which could be used for differentiating healthy and diseased samples. SMO/SVM and Logit Boost further followed J48 to achieve the classification accuracy.

Antibacterial, Antifungal, Antioxidant, and Docking Studies of Potential Dinaphthodiospyrols from Diospyros lotus Linn Roots.

The main aims of this investigation were the isolation of dimeric naphthoquinones, a new class of dinaphthodiospyrols (1–7), from chloroform fractions and screening them for antibacterial, antifungal, and antioxidant potential. The susceptibility of the isolated compounds, namely, dinaphthodiospyrol A (1), dinaphthodiospyrol B (2), dinaphthodiospyrol C (3), dinaphthodiospyrol D (4), dinaphthodiospyrol E (5), dinaphthodiospyrol F (6), and dinaphthodiospyrol G (7) was assessed for antibacterial potential using well diffusion methods. The isolated compounds showed excellent antibacterial activity against selected bacterial strains, including Gram-positive Bacillus subtilis, Streptococcus epidermis, and Bacillus subtilis, and Gram-negative bacteria Klebsiella pneumonia with the zones of inhibition 6 to 26 nm. The standard drug Imipenem showed a maximum inhibitory zone 30 to 35 nm. Similarly, the isolated compounds were screened for antifungal properties, which showed an excellent reduction in the growth of selected fungal strain including Candida albicans, Aspergillus flavus, Fusarium solani, Trichyton logifusus, Microsporum canis, andCandida glabrata. Among all the screened compounds, 7 exhibited good activity (30–49 mm), followed by compounds 5 and 6, (35–46 mm), while compounds 1–4 showed a moderate effect (8–28 mm) against the selected fungal strain against miconazole which showed potent effects (101–110.98 mm). The isolated compounds were also screened for 1, 1-diphenyl-2-picrylhydrazyl (DPPH) activity. In vitro-based free radical was employed using ascorbic acid as a standard antioxidant. The tested compounds (1–7) exhibited significant antioxidant activity in a concentration-dependent manner. The dinaphthodiospyrol 7 exhibited 97.32% scavenging activity, followed by dinaphthodiospyrol 6, 92.01%, and compounds 5 and 4 with 89.90 and 88.43% scavenging activity at 100 μg/mL, respectively; ascorbic acid showed 96.45% scavenging effect. Furthermore, docking analysis was performed to know the exact binding mode of the tetra-substituted derivatives of dinaphthodiospyrols to the selected target proteins. From the docking analysis, it was found that the docking results are well correlated with the experimental observations. In conclusion, the dinaphthodiospyrols exhibited excellent antibacterial, antifungal, and free radical scavenging potential.

The clinical potential of prm-PASEF mass spectrometry

ABSTRACT Introduction The continuous technical improvement in sensitivity and specificity placed mass spectrometry as an alternative method for analyzing clinical samples. In parallel to the rapid development of discovery proteomics, targeted acquisition has been implemented as a complementary option for measuring a small set of proteins with high sensitivity and robustness in a large sample cohort. The combination of trapped ion mobility with a rapid time-of-flight (TOF) mass spectrometer improves the sensitivity even further and triggers the development of prm-PASEF. Areas covered This article discusses the development of prm-PASEF and its advantages over the existing targeted and discovery methods for analyzing clinical samples. We are also highlighting the different requirements for the use of prm-PASEF on clinical samples. Expert opinion prm-PASEF takes advantage of a dual ion-mobility trap enabling highly multiplexed targeted acquisition. It allows the implementation of a short chromatographic separation setup without sacrificing the number of targeted peptides. Analyzing clinical samples by prm-PASEF holds the promise to significantly improve throughput while maintaining sensitivity to detect the selected target proteins.

Computational structure characterization, nonlinear optical properties and antitumor activities of Nickel(II) complexes containing alkoxy-derived dicyandiamide ligands

[Ni(dcda-O-Me) 2 ] 2+ (1) , [Ni(dcda-O-Et) 2 ] 2+ (2) , [Ni(dcda-O-nPr) 2 ] 2+ (3) , and [Ni(dcda-O-nBu) 2 ] 2+ (4) complexes (dcda-O-R is dicyandiamide ligands with alkoxy-derived) have been optimized in the gas phase at B3LYP/LANL2DZ/6-31+G(d,p) level. Computational structure characterization has been performed from the structural parameters, IR spectra, 1 H-NMR, 13 C-NMR chemical shift values. It has been found that the central metal atom geometry in the complexes is a distorted square plane. Some electronic structure descriptors of the complexes are calculated in the gas phase and nonlinear optical properties are predicted. Complex 1 is found as the most suitable compound to produce optical material. The complexes are optimized at the same level in the aqueous phase to determine antitumor activity. Some electronic structure descriptors are calculated and molecular docking calculations are made against the 3WZE protein. According to the calculated electronic structure descriptors and molecular docking results, it is found that the complex 3 has the highest antitumor activity against the selected target protein.

A Comprehensive in vitro and in silico Analysis of Nematicidal Action of Essential Oils.

Nematicidal potential of essential oils (EOs) has been widely reported. Terpenoids present in most of the essential oils have been reported responsible for their bioactivity though very less is known about their modes of action. In the present study, an in vitro screening of nine Eos, namely, Citrus sinensis (OEO), Myrtus communis (MTEO), Eucalyptus citriodora (CEO), Melaleuca alternifolia (TEO), Acorus calamus (AEO), Commiphora myrrha (MREO), Cymbopogon nardus (CNEO), Artemisia absinthium (WEO), and Pogostemon cablin (PEO) against Meloidogyne incognita revealed OEO, CNEO, and TEO as most effective with LC50 39.37, 43.22, and 76.28 μg ml–1 respectively. EOs had varying compositions of mono- and sesquiterpenes determined by gas chromatography-mass spectrometry (GC-MS) analysis. The in silico molecular interactions screening of major EO constituents and the seven selected target proteins of the nematode indicated highest binding affinity of geraniol-ODR1 (odorant response gene 1) complex (ΔG = -36.9 kcal mol–1), due to extensive H-bonding, hydrophobic and π-alkyl interactions. The relative binding affinity followed the order: geraniol-ODR1 > β-terpineol-ODR1 > citronellal-ODR1 > l-limonene-ODR1 > γ-terpinene-ODR1. Taken together, the cumulative in vitro and computational bioefficacy analysis related to the chemoprofiles of EOs provides useful leads on harnessing the potential of EOs as bionematicides. The insight on biochemical ligand–target protein interactions described in the present work will be helpful in logical selection of biomolecules and essential oils for development of practically viable bionematicidal products.

Anti-Tuberculosis Activity in Punica granatum: In silico Validation and Identification of Lead Molecules

Discovery of novel drug against tuberculosis is inevitable since resistant bacterial strains are evolved against existing drugs and rapidly active single drug in short period is necessary for effective treatment. When compared to synthetic drugs, natural drugs particularly phytochemicals induce less side effects and long term stability. In Indian traditional medicine, several plant species have been used for treating tuberculosis and each plant species contains a plethora of phytochemicals. The efficacy of such treatment system and identification of the phytochemical with drug activity from plants has been seldom investigated scientifically. In this backdrop, the authors have validated the efficacy of anti-tuberculosis activity and identified lead molecule from a widely used plant species against several disease including tuberculosis, viz Punica granatum L. The four promising target proteins viz mycolyltransferase antigen protein 85C involved in cord factor synthesis, filamentous temperature sensitive protein Z involved in bacterial cell division, pantothenate kinase involved in co-enzyme A pathway and decaprenylphosphoryl β-D-ribofuranose-2 epimerase involved in the synthesis of virulent factor arabinan were docked with 243 phytochemicals derived from Punica granatum. The docked molecules having binding energy ≤-6 kcal/ mol were considered as active/hit molecules. The docked results showed that out of 243 phytochemicals, 126 have inhibitory activity on all selected target proteins. Further docking study using Glide and absorption, distribution, metabolism, excretion and toxicity studies revealed that the compound derived from the lowers, pomegranatate can be recommended as the best lead compound against tuberculosis.

Maximizing cohesion and separation for detecting protein functional modules in protein-protein interaction networks.

Protein Function Module (PFM) identification in Protein-Protein Interaction Networks (PPINs) is one of the most important and challenging tasks in computational biology. The quick and accurate detection of PFMs in PPINs can contribute greatly to the understanding of the functions, properties, and biological mechanisms in research on various diseases and the development of new medicines. Despite the performance of existing detection approaches being improved to some extent, there are still opportunities for further enhancements in the efficiency, accuracy, and robustness of such detection methods. Based on the uniqueness of the network-clustering problem in the context of PPINs, this study proposed a very effective and efficient model based on the Lin-Kernighan-Helsgaun algorithm for detecting PFMs in PPINs. To demonstrate the effectiveness and efficiency of the proposed model, computational experiments are performed using three different categories of species datasets. The computational results reveal that the proposed model outperforms existing detection techniques in terms of two key performance indices, i.e., the degree of polymerization inside PFMs (cohesion) and the deviation degree between PFMs (separation), while being very fast and robust. The proposed model can be used to help researchers decide whether to conduct further expensive and time-consuming biological experiments and to select target proteins from large-scale PPI data for further detailed research.

In silico molecular docking analysis for repurposing therapeutics against multiple proteins from SARS-CoV-2

SARS-CoV-2 has devastated the world with its rapid spread and fatality. The researchers across the globe are struggling hard to search a drug to treat this infection. Understanding the time constraint, the best approach is to study clinically approved drugs for control of this deadly pandemic of COVID 19. The repurposing of such drugs can be supported with the study of molecular interactions to enhance the possibility of application. The present work is a molecular docking study of proteins responsible for viral propagation namely 3Clpro, Nsp10/16, Spike protein, SARS protein receptor binding domain, Nsp 9 viral single strand binding protein and viral helicase. The protein through virus enters the host cell-human angiotensin-converting enzyme 2 (ACE2) receptor, is also used as a target for molecular docking. The docking was done with most discussed drugs for SARS-CoV-2 like Ritonavir, Lopinavir, Remdesivir, Chloroquine, Hydroxychloroquine (HCQ), routine antiviral drugs like Oseltamivir and Ribavirin. In addition, small molecules with anti-inflammatory actions like Mycophenolic acid (MPA), Pemirolast, Isoniazid and Eriodictyol were also tested. The generated data confirms the potential of Ritonavir, Lopinavir and Remdesivir as a therapeutic candidate against SARS-CoV-2. It is observed that Eriodictyol binds to almost all selected target proteins with good binding energy, suggesting its importance in treatment of COVID 19. Molecular interactions of Ritonavir, Lopinavir and Remdesivir against SARS-CoV-2 proteins enhanced their potential as a candidate drug for treatment of COVID-19. Eriodictyol had emerged as a new repurposing drug that can be used in COVID-19.

<i>In Silico</i> Study on Interaction and Preliminary Toxicity Prediction of <i>Eleutherine americana</i> Components as an Antifungal and Antitoxoplasmosis Candidate

Red bulbs of Eleutherine americana (Aubl.) Merr. ex K. Heyne has been known for its high content of naphthoquinones that have antifungal and antiparasitic activities. In this research, in silico interaction study was performed between 31 compounds reported to be found in E. americana with the selected target proteins for antifungal and antitoxoplasmosis activity using the molecular docking method. An ORPs (OSBP-related proteins), Osh4 (PDB ID: 1ZHX), and N-myristoyltransferase (Nmt, PDB ID: 1IYL) were used as the antifungal target proteins. Toxoplasma gondii purine nucleoside phosphorylase (TgPNP, PDB ID: 3MB8) and calcium-dependent protein kinase-1 (TgCDPK1, PDB ID: 4M84) were used as antitoxoplasmosis target proteins. Three-dimensional structures of the test compounds were made and optimized using GaussView 6.0 and Gaussian 09W. The target proteins were prepared using the Discovery Studio 2016 Program. Aquatic toxicity prediction as the preliminary assessment of the safety of the compounds was performed using ECOSAR v2.0. The results suggest that the compound having both the smallest free binding energy compared with positive control and other test compounds and low predicted toxicity is β-sitosterol with a free binding energy of ‒11.55 and ‒11.18 kcal/mol towards Osh4 and Nmt and ‒8.06 and ‒10.29 kcal/mol towards TgPNP and TgCDPK1, respectively.

Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.

O-Linked β-N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Strategies for selectively increasing O-GlcNAc levels on a target protein in cells would accelerate studies of this essential modification. Here, we report a generalizable strategy for introducing O-GlcNAc into selected target proteins in cells using a nanobody as a proximity-directing agent fused to O-GlcNAc transferase (OGT). Fusion of a nanobody that recognizes GFP (nGFP) or a nanobody that recognizes the four-amino acid sequence EPEA (nEPEA) to OGT yielded nanobody-OGT constructs that selectively delivered O-GlcNAc to a series of tagged target proteins (e.g., JunB, cJun, and Nup62). Truncation of the tetratricopeptide repeat domain as in OGT(4) increased selectivity for the target protein through the nanobody by reducing global elevation of O-GlcNAc levels in the cell. Quantitative chemical proteomics confirmed the increase in O-GlcNAc to the target protein by nanobody-OGT(4). Glycoproteomics revealed that nanobody-OGT(4) or full-length OGT produced a similar glycosite profile on the target protein JunB and Nup62. Finally, we demonstrate the ability to selectively target endogenous α-synuclein for O-GlcNAcylation in HEK293T cells. These first proximity-directed OGT constructs provide a flexible strategy for targeting additional proteins and a template for further engineering of OGT and the O-GlcNAc proteome in the future. The use of a nanobody to redirect OGT substrate selection for glycosylation of desired proteins in cells may further constitute a generalizable strategy for controlling a broader array of post-translational modifications in cells.

Theoretical and Experimental Spectroscopic Properties and Molecular Docking of F8BT p-Type Semiconducting Polymer

F8BT, which is highly conjugated with therapeutic proteins for light emitting and targeted drug delivery, has been investigated theoretically and experimentally. Transfer integral, reorganization energies and molecular orbitals (HOMO and LUMO) were examined for OLEDs features of mentioned polymer. The experimental vibrational frequencies were compared with the calculated frequencies and related bond stretching labeling in vibrational spectra was performed. Molecular docking studies were performed for the binding energies of certain drug proteins in order to provide stable dispersion for drug delivery of F8BT, a biodegradable and non-cytotoxic nanoparticle. It was found that the hole transfer rate is larger than the electron transfer rate and the F8BT can be used as a hole transfer materials. The HOMO and LUMO molecular orbitals of F8BT were found to be –5.68 and –2.76 eV, respectively. F8BT solution dissolved in chloroform prepared using vortex mixer and FTIR spectra have been taken from it. Experimental FTIR results are fairly agreement with the theoretical results. From all the results it can be concluded that the F8BT molecule could be a good candidate for luminescent materials and can be used as a semiconducting systems. F8BT may have the potential to increase the stability of selected target proteins, circulatory times in the body, and permeability through cell membranes.

Ligand-based pharmacophore modeling and docking studies on vitamin D receptor inhibitors.

In recent years, pharmacophore modeling and molecular docking approaches have been extensively used to characterize the structural requirements and explore the conformational space of a ligand in the binding pocket of the selected target protein. Herein, we report a pharmacophore modeling and molecular docking of 45 compounds comprising of the indole scaffold as vitamin D receptor (VDR) inhibitors. Based on the selected best hypothesis (DRRRR.61), an atom-based three-dimensional quantitative structure-activity relationships model was developed to rationalize the structural requirement of biological activity modulating components. The developed model predicted the binding affinity for the training set and test set with R2(training) = 0.8869 and R2(test) = 0.8139, respectively. Furthermore, molecular docking and dynamics simulation were performed to understand the underpinning of binding interaction and stability of selected VDR inhibitors in the binding pocket. In conclusion, the results presented here, in the form of functional and structural data, agreed well with the proposed pharmacophores and provide further insights into the development of novel VDR inhibitors with better activity.

Identification of the Active Constituents and Significant Pathways of Guizhi-Shaoyao-Zhimu Decoction for the Treatment of Diabetes Mellitus Based on Molecular Docking and Network Pharmacology.

This study was designed to explore the active compounds and significant pathways of Guizhi-Shaoyao-Zhimu decoction (GSZD) for treating diabetes mellitus using molecular docking combined with network pharmacology. Chemical constituents of GSZD and diabetes-related target proteins were collected from various databases. Then, compounds were filtered by Lipinski's and Veber's rules with Discovery studio software. The "Libdock" module was used to carry out molecular docking, and LibDockScores, default cutoff values for hydrogen bonds, and van der Waals interactions were recorded. LibDockScore of the target protein and its prototype ligand was considered as the threshold, and compounds with higher LibDockScores than the threshold were regarded as the active constituents of GSZD. Cytoscape software was used to construct the herb-active molecule-target interaction network of GSZD. ClueGO and CluePedia were applied to enrich the analysis of the biological functions and pathways of GSZD. A total of 275 potential active compounds with 57 possible pathways in GSZD were identified by molecular docking combined with network pharmacology. TEN, INSR, PRKAA2, and GSK3B are the four most important target proteins. Gancaonin E, 3'-(γ,γ-dimethylallyl)-kievitone, aurantiamide, curcumin and 14-O-cinnamoylneoline, could interact with more than 14 of the selected target proteins. Besides, 57 potential pathways of GSZD were identified, such as insulin signaling pathway, metabolites and energy regulation, glucose metabolic process regulation, and positive regulation of carbohydrate metabolic process, etc. Conclusion: These results showed that molecular docking combined with network pharmacology is a feasible strategy for exploring bioactive compounds and mechanisms of Chinese medicines, and GSZD can be used to effectively treat diabetes through multi-components and multi-targets & pathways.

Label-Free Interactome Analysis Revealed an Essential Role of CUL3-KEAP1 Complex in Mediating the Ubiquitination and Degradation of PHD2.

Prolyl hydroxylase domain-containing protein 2 (PHD2/EGLN1) is a key regulatory enzyme that plays a fundamental role in the cellular hypoxic response pathway, mediating proline hydroxylation-dependent protein degradation of selected target proteins. However, the regulation of PHD2 homeostasis at the protein level is not well understood. Here, we perform label-free quantitative interactome analysis through immunoprecipitation coupled with mass spectrometry analysis. To minimize the side effects caused by ectopic overexpression, in HeLa cells, we stably overexpressed Flag-tagged PHD2 while suppressing the endogenous PHD2 by using an shRNA targeting its 3' UTR region. We identified and validated Cullin 3 as a novel PHD2 interactor in vivo. Through candidate screening, we further identified CUL3-KEAP1 E3 ubiquitin ligase complex as the major enzyme that regulates PHD2 degradation. Overexpression of either CUL3, KEAP1, or both significantly increases PHD2 ubiquitination and reduces PHD2 protein abundance. The knockdown of CUL3 or KEAP1 decreased PHD2 ubiquitination and inhibited PHD2 degradation. Accordingly, loss of the CUL3-KEAP1 complex under hypoxia promoted PHD2 stabilization and led to significantly reduced abundance of the PHD2 target, hypoxia-inducible factor 1A (HIF1A). Thus, CUL3-KEAP1 is an essential pathway that regulates PHD2 ubiquitination and degradation in cells.

Brain protein changes in Mecp2 mouse mutant models: Effects on disease progression of Mecp2 brain specific gene reactivation

Rett syndrome (RTT) is a leading cause of severe intellectual disability in females, caused by de novo loss-of function mutations in the X-linked methyl-CpG binding protein 2 (MECP2). To better investigate RTT disease progression/pathogenesis animal models of Mecp2 deficiency have been developed. Here, Mecp2 mouse models are employed to investigate the role of protein patterns in RTT. A proteome analysis was carried out in brain tissue from i) Mecp2 deficient mice at the pre-symptomatic and symptomatic stages and, ii) mice in which the disease phenotype was reversed by Mecp2 reactivation. Several proteins were shown to be differentially expressed in the pre-symptomatic (n = 18) and symptomatic (n = 20) mice. Mecp2 brain reactivated mice showed wild-type comparable levels of expression for twelve proteins, mainly related to proteostasis (n = 4) and energy metabolic pathways (n = 4). The remaining ones were found to be involved in redox homeostasis (n = 2), nitric oxide regulation (n = 1), neurodevelopment (n = 1). Ten out of twelve proteins were newly linked to Mecp2 deficiency. Our study sheds light on the relevance of the protein-regulation of main physiological process in the complex mechanisms leading from Mecp2 mutation to the RTT clinical phenotype. SignificanceWe performed a proteomic study of a Mecp2stop/y mouse model for Rett syndrome (RTT) at the pre-symptomatic and symptomatic Mecp2 deficient mice stage and for the brain specific reactivated Mecp2 model. Our results reveal major protein expression changes pointing out to defects in proteostasis or energy metabolic pathways other than, to a lesser extent, in redox homeostasis, nitric oxide regulation or neurodevelopment. The Mecp2 mouse rescued model provides the possibility to select target proteins more susceptible to the Mecp2 gene mutation, potential and promising therapeutical targets.

The Identification of Bioactive Compounds from Turbinaria ornata (Turner) J. Agaradh and Computational Studies

Aim/Background: The present work was carried out to identify some of the bioactive components present in the Brown seaweed Turbinaria ornata by GC-MS technique, and to ascertain its medicinal properties. Materials and Methods: GC-MS analysis of some of the potent volatile constituents present in the pet ether of Turbinaria ornata was performed. MD simulations were performed for complex structures of human secretory PLA2 and P38 kinase. GC-MS chromatogram showed peaks indicating the presence of various compounds of interest. The interpretation of the mass spectrum of GC-MS was done using the Database of Indian Institute of Crop Processing Technology (IICPT). Twenty compounds were identified in pet ether extract of Turbinaria ornata. All 20 compounds were screened using PASS online activity prediction server, for the possession of anti-inflammatory potency and the selected target proteins were subjected to molecular docking studies. MD simulations were also performed for the top listed compound 16 which was identified from D3P extract (2,3-Diphenylcyclopropyl)methyl phenyl sulfoxide, trans-). Similarly, the complex structure of PLA2 (phospho-ethanolamine, PE) and P38 kinase (3-(2-pyridine-4-ylethyl)-1H-indole) were simulated for comparative study. Results and Conclusion: Based on the in silico results, the binding affinities for compounds of T. ornata were judged against known standards for its capability to restrain inflammation and to promote possibility for scheming potential antiinflammatory lead from natural compounds were discussed.

Overexpression of hsa-miR-186 induces chromosomal instability in arsenic-exposed human keratinocytes

The mechanism of arsenic-induced skin carcinogenesis is not yet fully understood. Chromosomal instability contributes to aneuploidy and is a driving force in carcinogenesis. Arsenic causes mitotic arrest and induces aneuploidy. hsa-miR-186 overexpression is associated with metastatic cancers as well as arsenic-induced squamous cell carcinoma and is reported to target several mitotic regulators. Decreased levels of these proteins can dysregulate chromatid segregation contributing to aneuploidy. This work investigates the potential aneuploidogenic role of hsa-miR-186 in arsenic carcinogenesis. Clones of immortalized human keratinocytes (HaCaT) stably transfected with a hsa-miR-186 expression or empty vector were isolated. Three clones with high and low hsa-miR-186 expression determined by RT-qPCR were selected for further analysis and cultured with 0 or 100 nM NaAsO2 for 8 weeks. Analysis of mitoses revealed that chromosome number and structural abnormalities increased in cells overexpressing hsa-miR-186 and were further increased by arsenite exposure. Double minutes were the dominant structural aberrations. The peak number of chromosomes also increased. Cells with >220 to >270 chromosomes appeared after 2 months in hsa-miR-186 overexpressing cells, indicating multiple rounds of endomitosis had occurred. The fraction of cells with increased chromosome number or structural abnormalities did not increase in passage matched control cells. Levels of selected target proteins were determined by western blot. Expression of BUB1, a predicted hsa-miR-186 target was suppressed in hsa-miR-186 overexpressing clones, but increased with arsenite exposure. CDC27 remained constant under all conditions. These results suggest that overexpression of miR-186 in arsenic exposed tissues likely induces aneuploidy contributing to arsenic-induced carcinogenesis.

Molecular docking studies of bioactive compounds from Abutilon hirtum (Lam). Sweet (Malvaceae)

The present investigation was aimed at controlling metastasis and cell proliferation in cancer by molecular docking of the previously isolated molecules of Abutilon hirtum with the targets Urokinase plasminogen activator (uPA) and its receptor urokinase (uPA)-type plasminogen activator receptor (uPAR) protein. Among all the ligands docked with the two selected target protein molecules, 2, 4-dihydroxybenzoic acid had an efficient docking score of-4.94 with target protein uPA. Likewise it showed a docking score of-4.03 with three bonds with uPAR. 3, 4, 5-trihydroxybenzoic acid interacted with uPA with a G-Score of-5.05 whereas it had very less interaction with uPAR. The standard control drug Docetaxel formed two hydrogen bonds with uPAR; with very least G Score of-1.21. It showed no significant interaction with uPA. The ligand molecules selected for docking interacted with the selected protein target molecules at their active sites (involved in protein-protein, uPA-uPAR interaction) and nearby amino acid residues from the setup made from Grid Generation Panel. The results clearly indicated that the ligand molecules can be used as potential small molecule inhibitors of the drug targets uPAand uPAR that can possibly control the metastasis or other related factors responsible for the spreading of human prostate cancer

Exploring Highly Antigenic Protein of Campylobacter jejuni for Designing Epitope Based Vaccine: Immunoinformatics Approach

Campylobacter jejuni is a spiral-shaped Gram-negative and microaerophilic bacteria that causes bacterial diarrhea worldwide. Due to its complicated antigenic nature, lack of proper animal models, and a poor understanding of its pathogenicity there is no vaccine against C. jejuni. The most effective way of reducing the number of Campylobacter infections is by developing protective vaccines for humans. Due to the increasing resistance against antibiotics of bacterial strains epitopes-based vaccine could be the best approach to trigger an effective immune response. Immunoinformatics methods can be an alternative approach for developing epitope-based vaccine which is able to elucidate humoral and cell-mediated immune response inside the host body. Reverse vaccinology approach analyses the entire protein sequences of the pathogen using bioinformatics tools to select target proteins for their high-throughput expression and validation. Here in this research study, three epitopes MSNVYAYRF, LSDDINLNI and ATSTSTITL have been identified as the most potential epitopes binding with HLA-B*58:01, HLA-A*01:01 and HLA-B*07:02 MHC class I allele, respectively. With the help of Autodock vina, these three epitopes have shown the lowest binding energies and form the most complex docked structure covering the maximum number of populations worldwide. Thus, we suggest these peptides may have a good potential if further presented for experimental analysis and can be proved to be helpful against C. jejuni infections causing diarrhea.

Pseudomonas aeruginosa nfuA: Gene regulation and its physiological roles in sustaining growth under stress and anaerobic conditions and maintaining bacterial virulence.

The role of the nfuA gene encoding an iron-sulfur ([Fe-S]) cluster-delivery protein in the pathogenic bacterium Pseudomonas aeruginosa was investigated. The analysis of nfuA expression under various stress conditions showed that superoxide generators, a thiol-depleting agent and CuCl2 highly induced nfuA expression. The expression of nfuA was regulated by a global [2Fe-2S] cluster containing the transcription regulator IscR. Increased expression of nfuA in the ΔiscR mutant under uninduced conditions suggests that IscR acts as a transcriptional repressor. In vitro experiments revealed that IscR directly bound to a sequence homologous to the Escherichia coli Type-I IscR-binding motifs on a putative nfuA promoter that overlapped the -35 element. Binding of IscR prevented RNA polymerase from binding to the nfuA promoter, leading to repression of the nfuA transcription. Physiologically, deletion of nfuA reduced the bacterial ability to cope with oxidative stress, iron deprivation conditions and attenuated virulence in the Caenorhabditis elegans infection model. Site-directed mutagenesis analysis revealed that the conserved CXXC motif of the Nfu-type scaffold protein domain at the N-terminus was required for the NfuA functions in conferring the stress resistance phenotype. Furthermore, anaerobic growth of the ΔnfuA mutant in the presence of nitrate was drastically retarded. This phenotype was associated with a reduction in the [Fe-S] cluster containing nitrate reductase enzyme activity. However, NfuA was not required for the maturation of [Fe-S]-containing proteins such as aconitase, succinate dehydrogenase, SoxR and IscR. Taken together, our results indicate that NfuA functions in [Fe-S] cluster delivery to selected target proteins that link to many physiological processes such as anaerobic growth, bacterial virulence and stress responses in P. aeruginosa.